Production of syringyl lignin in gymnosperms

ABSTRACT

The present invention relates to a method for producing syringyl lignin in gymnosperms. The production of syringyl lignin in gymnosperms is accomplished by genetically transforming a gymnosperm genome, which does not normally contain genes which code for enzymes necessary for production of syringyl lignin, with DNA which codes for enzymes found in angiosperms associated with production of syringyl lignin. The expression of the inserted DNA is mediated using host promoter regions in the gymnosperm. In addition, genetic sequences which code for gymnosperm lignin anti-sense mRNA may be incorporated into the gymnosperm genome in order to suppress the formation of the less preferred forms of lignin in the gymnosperm such as guaiacyl lignin

This application claims the benefit of U.S. Provisional Application No. 60/033,381, filed Dec. 16, 1996. The invention relates to the molecular modification of gymnosperms in order to cause the production of syringyl units during lignin biosynthesis and to production and propagation of gymnosperms containing syringyl lignin.

FIELD OF THE INVENTION Background of the Invention

Lignin is a major part of the supportive structure of most woody plants including angiosperm and gymnosperm trees which in turn are the principal sources of fiber for making paper and cellulosic products. In order to liberate fibers from wood structure in a manner suitable for making many grades of paper, it is necessary to remove much of the lignin from the fiber/lignin network. Lignin is removed from wood chips by treatment of the chips in an alkaline solution at elevated temperatures and pressure in an initial step of papermaking processes. The rate of removal of lignin from wood of different tree species varies depending upon lignin structure. Three different lignin structures have been identified in trees: p-hydroxyphenyl, guaiacyl and syringyl, which are illustrated in FIG. 1.

Angiosperm species, such as Liquidambar styraciflua L. [sweetgum], have lignin composed of a mixture of guaiacyl and syringyl monomer units. In contrast, gymnosperm species such as Pinus taeda L. [loblolly pine] have lignin which is devoid of syringyl monomer units. Generally speaking, the rate of delignification in a pulping process is directly proportional to the amount of syringyl lignin present in the wood. The higher delignification rates associated with species having a greater proportion of syringyl lignin result in more efficient pulp mill operations since the mills make better use of energy and capital investment and the environmental impact is lessened due to a decrease in chemicals used for delignification.

It is therefore an object of the invention to provide gymnosperm species which are easier to delignify in pulping processes.

Another object of the invention is to provide gymnosperm species such as loblolly pine which contain syringyl lignin.

An additional object of the invention is to provide a method for modifying genes involved in lignin biosynthesis in gymnosperm species so that production of syringyl lignin is increased while production of guaiacyl lignin is suppressed.

Still another object of the invention is to produce whole gymnosperm plants containing genes which increase production of syringyl lignin and repress production of guaiacyl lignin.

Yet another object of the invention is to identify, isolate and/or clone those genes in angiosperms responsible for production of syringyl lignin.

A further object of the invention is to provide, in gymnosperms, genes which produce syringyl lignin.

Another object of the invention is to provide a method for making an expression cassette insertable into a gymnosperm cell for the purpose of inducing formation of syringyl lignin in a gymnosperm plant derived from the cell.

Definitions

The term “promoter” refers to a DNA sequence in the 5′ flanking region of a given gene which is involved in recognition and binding of RNA polymerase and other transcriptional proteins and is required to initiate DNA transcription in cells.

The term “constitutive promoter” refers to a promoter which activates transcription of a desired gene, and is commonly used in creation of an expression cassette designed for preliminary experiments relative to testing of gene function. An example of a constitutive promoter is 35S CaMV, available from Clonetech.

The term “expression cassette” refers to a double stranded DNA sequence which contains both promoters and genes such that expression of a given gene is achieved upon insertion of the expression cassette into a plant cell.

The term “plant” includes whole plants and portions of plants, including plant organs (e.g. roots, stems, leaves, etc.)

The term “angiosperm” refers to plants which produce seeds encased in an ovary. A specific example of an angiosperm is Liquidambar styraciflua (L.)[sweetgum]. The angiosperm sweetgum produces syringyl lignin.

The term “gymnosperm” refers to plants which produce naked seeds, that is, seeds which are not encased in an ovary. A specific example of a gymnosperm is Pinus taeda (L.)[loblolly pine]. The gymnosperm loblolly pine does not produce syringyl lignin.

SUMMARY OF THE INVENTION

With regard to the above and other objects, the invention provides a method for inducing production of syringyl lignin in gymnosperms and to gymnosperms which contain syringyl lignin for improved delignification in the production of pulp for papermaking and other applications. In accordance with one of its aspects, the invention involves cloning an angiosperm DNA sequence which codes for enzymes involved in production of syringyl lignin monomer units, fusing the angiosperm DNA sequence to a lignin promoter region to form an expression cassette, and inserting the expression cassette into a gymnosperm genome.

Enzymes required for production of syringyl lignin in an angiosperm are obtained by deducing an amino acid sequence of the enzyme, extrapolating an mRNA sequence from the amino acid sequence, constructing a probe for the corresponding DNA sequence and cloning the DNA sequence which codes for the desired enzyme. A promoter region specific to a gymnosperm lignin biosynthesis gene is identified by constructing a probe for a gymnosperm lignin biosynthesis gene, sequencing the 5′ flanking region of the DNA which encodes the gymnosperm lignin biosynthesis gene to locate a promoter sequence, and then cloning that sequence.

An expression cassette is constructed by fusing the angiosperm syringyl lignin DNA sequence to the gymnosperm promoter DNA sequence. Alternatively, the angiosperm syringyl lignin DNA is fused to a constitutive promoter to form an expression cassette. The expression cassette is inserted into the gymnosperm genome to transform the gymnosperm genome. Cells containing the transformed genome are selected and used to produce a transformed gymnosperm plant containing syringyl lignin.

In accordance with the invention, the angiosperm gene sequences bi-OMT, 4CL, P450-1 and P-450-2 have been determined and isolated as associated with production of syringyl lignin in sweetgum and lignin promoter regions for the gymnosperm loblolly pine have been determined to be the 5′ flanking regions for the 4CL1B, 4CL3B and PAL gymnosperm lignin genes. Expression cassettes containing sequences of selected genes from sweetgum have been inserted into loblolly pine embryogenic cells and presence of sweetgum genes associated with production of syringyl lignin has been confirmed in daughter cells of the resulting loblolly pine embryogenic cells.

The invention therefore enables production of gymnosperms such as loblolly pine containing genes which code for production of syringyl lignin, to thereby produce in such species syringyl lignin in the wood structure for enhanced pulpability.

BRIEF DESCRIPTION OF THE DRAWINGS

The above and other aspects of the invention will now be further described in the following detailed specification considered in conjunction with the following drawings in which:

FIG. 1 illustrates a generalized pathway for lignin synthesis; and

FIGS. 2A-2E illustrate a bifunctional-O-methyl transferase (bi-OMT) gene sequence involved in the production of syringyl lignin in an angiosperm (SEQ ID 5 coding SEQ ID 6);

FIGS. 3A-3G illustrate a 4-coumarate CoA ligase (4CL) gene sequence involved in the production of syringyl lignin in an angiosperm (SEQ ID 7 coding SEQ ID 8);

FIG. 4 illustrates a ferulic acid-5-hydroxylase (P450-1) gene sequence involved in the production of syringyl lignin in an angiosperm (SEQ ID 1 coding SEQ ID 2);

FIG. 5 illustrates a ferulic acid-5-hydroxylase (P450-2) gene sequence involved in the production of syringyl lignin in an angiosperm (SEQ ID 3 coding SEQ ID 4);

FIG. 6 illustrates nucleotide sequences of the 5′ flanking region of the loblolly pine 4CL1B gene showing the location of regulatory elements for lignin biosynthesis (SEQ ID 10);

FIGS. 7A-7B illustrate nucleotide sequences of the 5′ flanking region of the loblolly pine 4CL3B gene showing the location of regulatory elements for lignin biosynthesis (SEQ ID 11);

FIGS. 8A-8B illustrate nucleotide sequences of the 5′ flanking region of loblolly pine PAL gene showing the location of regulatory elements for lignin biosynthesis (SEQ ID 9);

FIG. 9 illustrates a PCR confirmation of the sweetgum P450-1 gene sequence in transgenic loblolly pine cells; and

DETAILED DESCRIPTION OF THE INVENTION

In accordance with the invention, a method is provided for modifying a gymnosperm genome, such as the genome of a loblolly pine, so that syringyl lignin will be produced in the resulting plant, thereby enabling cellulosic fibers of the same to be more easily separated from lignin in a pulping process. In general, this is accomplished by fusing one or more angiosperm DNA sequences (referred to at times herein as the “ASL DNA sequences”) which are involved in production of syringyl lignin to a gymnosperm lignin promoter region (referred to at times herein as the “GL promoter region”) specific to genes involved in gymnosperm lignin biosynthesis to form a gymnosperm syringyl lignin expression cassette (referred to at times herein as the “GSL expression cassette”). Alternatively, the one or more ASL DNA sequences are fused to one or more constitutive promoters to form a GSL expression cassette.

The GSL expression cassette preferably also includes selectable marker genes which enable transformed cells to be differentiated from untransformed cells. The GSL expression cassette containing selectable marker genes is inserted into the gymnosperm genome and transformed cells are identified and selected, from which whole gymnosperm plants may be produced which exhibit production of syringyl lignin.

To suppress production of less preferred forms of lignin in gymnosperms, such as guaiacyl lignin, genes from the gymnosperm associated with production of these less preferred forms of lignin are identified, isolated and the DNA sequence coding for anti-sense mRNA (referred to at times herein as the “GL anti-sense sequence”) for these genes is produced. The DNA sequence coding for anti-sense mRNA is then incorporated into the gymnosperm genome, which when expressed bind to the less preferred guaiacyl gymnosperm lignin mRNA, inactivating it.

Further features of these and various other steps and procedures associated with practice of the invention will now be described in more detail beginning with identification and isolation of ASL DNA sequences of interest for use in inducing production of syringyl lignin in a gymnosperm.

I. DETERMINATION OF DNA SEQUENCE FOR GENES ASSOCIATED WITH PRODUCTION OF SYRINGYL LIGNIN

The general biosynthetic pathway for production of lignin has been postulated as shown in FIG. 1. From FIG. 1, it can be seen that the genes CCL, OMT and F5H (which is from the class of P450 genes) may play key roles in production of syringyl lignin in some plant species, but their specific contributions and mechanisms remain to be positively established. It is suspected that the CCL, OMT and F5H genes may have specific equivalents in a specific angiosperm, such as sweetgum. Accordingly, one aim of the present invention is to identify, sequence and clone specific genes of interest from an angiosperm such as sweetgum which are involved in production of syringyl lignin and to then introduce those genes into the genome of a gymnosperm, such as loblolly pine, to induce production of syringyl lignin.

Genes of interest may be identified in various ways, depending on how much information about the gene is already known. Genes believed to be associated with production of syringyl lignin have already been sequenced from a few angiosperm species, viz, CCL and OMT.

DNA sequences of the various CCL and OMT genes are compared to each other to determine if there are conserved regions. Once the conserved regions of the DNA sequences are identified, oligo-dT primers homologous to the conserved sequences are synthesized. Reverse transcription of the DNA-free total RNA which was purified from sweetgum xylem tissue, followed by double PCR using gene-specific primers, enables production of probes for the CCL and OMT genes.

A sweetgum cDNA library is constructed in a host, such as lambda ZAPII, available from Stratagene, of LaJolla, Calif., using poly(A)+ RNA isolated from sweetgum xylem, according to the methods described by Bugos et al. (1995 Biotechniques 19:734-737). The above mentioned probes are used to assay the sweetgum cDNA library to locate cDNA which codes for enzymes involved in production of syringyl lignin. Once a syringyl lignin sequence is located, it is then cloned and sequenced according to known methods which are familiar to those of ordinary skill.

In accordance with the invention, two sweetgum syringyl lignin genes have been determined using the above-described technique. These genes have been designated 4CL and bi-OMT. The sequence obtained for the sweetgum syringyl lignin gene, designated bi-OMT, is illustrated in FIG. 2 (SEQ ID 5 and 6). The sequence obtained for the sweetgum syringyl lignin gene, designated 4CL, is illustrated in FIG. 3 (SEQ ID 7 and 8).

An alternative procedure was employed to identify the F5H equivalent genes in sweetgum. Because the DNA sequences for similar P450 genes from other plant species were known, probes for the P450 genes were designed based on the conserved regions found by comparing the known sequences for similar P450 genes. The known P450 sequences used for comparison include all plant P450 genes in the GenBank database. Primers were designed based on two highly conserved regions which are common to all known plant P450 genes. The primers were then used in a PCR reaction with the sweetgum cDNA library as a template. Once P450-like fragments were located, they were amplified using standard PCR techniques, cloned into a pBluescript vector available from Clonetech of Palo Alto, Calif. and transformed into a DH5.alpha. E. coli strain available from Gibco BRL of Gaithersburg, Md.

After E. coli colonies were tested in order to determine that they contained the P450-like DNA fragments, the fragments were sequenced. Several P450-like sequences were located in sweetgum using the above described technique. One P450-like sequence was sufficiently different from other known P450 sequences to indicate that it represented a new P450 gene family. This potentially new P450 cDNA fragment was used as a probe to screen a full length clone from the sweetgum xylem library. These putative hydroxylase P450 clones were designated P450-1 and P450-2. The sequence obtained for P450-1 and P450-2 are illustrated in FIG. 4 (SEQ ID 1 and 2) and FIG. 5 (SEQ ID 3 and 4).

II. IDENTIFICATION OF GL GENE PROMOTER REGIONS

In order to locate gymnosperm lignin promoter regions, probes are developed to locate lignin genes. After the-gymnosperm lignin gene is located, the portion of DNA upstream from the gene is sequenced, preferably using the GenomeWalker Kit, available from Clonetech. The portion of DNA upstream from the lignin gene will generally contain the gymnosperm lignin promoter region.

Gymnosperm genes of interest include CCL-like genes and PAL-like genes, which are believed to be involved in the production of lignin in gymnosperms. Preferred probe sequences are developed based on previously sequenced genes, which are available from the gene bank. The preferred gene bank accession numbers for the CCL-like genes include U39404 and U39405. A preferred gene bank accession number for a PAL-like gene is U39792. Probes for such genes are constructed according to methods familiar to those of ordinary skill in the art. A genomic DNA library is constructed and DNA fragments which code for gymnosperm lignin genes are then identified using the above mentioned probes. A preferred DNA library is obtained from the gymnosperm, Pinus taeda (L.)[Loblolly Pine], and a preferred host of the genomic library is Lambda DashII, available from Stratagene of LaJolla, Calif.

Once the DNA fragments which code for the gymnosperm lignin genes are located, the genomic region upstream from the gymnosperm lignin gene (the 5′ flanking region) was identified. This region contains the GL promoter. Three promoter regions were located from gymnosperm lignin biosynthesis genes. The first is the 5′ flanking region of the loblolly pine 4CL1B gene, shown in FIG. 6 (SEQ ID 10). The second is the 5′ flanking region of the loblolly pine gene 4CL3B, shown in FIG. 7 (SEQ ID 11). The third is the 5′ flanking region of the loblolly pine gene PAL, shown in FIG. 8 (SEQ ID 9).

III. FUSING THE GL PROMOTER REGION TO THE ASL DNA SEQUENCE

The next step of the process is to fuse the GL promoter region to the ASL DNA sequence to make a GSL expression cassette for insertion into the genome of a gymnosperm. This may be accomplished by standard techniques. In a preferred method, the GL promoter region is first cloned into a suitable vector. Preferred vectors are pGEM7Z, available from Promega, Madison, Wis. and SK available from Stratagene, of LaJolla, Calif. After the promoter sequence is cloned into the vector, it is then released with suitable restriction enzymes. The ASL DNA sequence is released with the same restriction enzyme(s) and purified.

The GL promoter region sequence and the ASL DNA sequence are then ligated such as with T4 DNA ligase, available from Promega, to form the GSL expression cassette. Fusion of the GL and ASL DNA sequence is confirmed by restriction enzyme digestion and DNA sequencing. After confirmation of GL promoter-ASL DNA fusion, the GSL expression cassette is released from the original vector with suitable restriction enzymes and used in construction of vectors for plant transformation.

IV. FUSING THE ASL DNA SEQUENCE TO A CONSTITUTIVE PROMOTER REGION

In an alternative embodiment, a standard constitutive promoter may be fused with the ASL DNA sequence to make a GSL expression cassette. For example, a standard constitutive promoter may be fused with P450-1 to form an expression cassette for insertion of P450-1 sequences into a gymnosperm genome. In addition, a standard constitutive promoter may be fused with P450-2 to form an expression cassette for insertion of P450-2 into a gymnosperm genome. A constitutive promoter for use in the invention is the double 35S promoter, available from Clonetech.

In the preferred practice of the invention using constitutive promoters, a suitable vector such as pBI221, is digested XbaI and HindIII to release the 35S promoter. At the same time the vector pHygro, available from International Paper, was disgested by XbaI and HindIII to release the double 35S promoter. The double 35S promoter was ligated to the previously digested pBI221 vector to produce a new pBI221 with the double 35S promoter. This new pBI221 was digested with SacI and SmaI, to release the GUS fragment. The vector is next treated with T4 DNA polymerase to produce blunt ends and the vector is self-ligated. This vector is then further digested with BamHI and XbaI, available from Promega. After the pBI221 vector containing the constitutive promoter region has been prepared, lignin gene sequences are prepared for insertion into the pBI221 vector.

The coding regions of sweetgum P450-1 or P450-2 are amplified by PCR using primer with restriction sites incorporated in the 5′ and 3′ ends. In one example, an XbaI site was incorporated at the 5′ end and a BamHI site was incorporated at the 3′ end of the sweetgum P450-1 or P450-2 genes. After PCR, the P450-1 and P450-2 genes were separately cloned into a TA vector available from Invitrogen. The TA vectors containing the P450-1 and P450-2 genes, respectively, were digested by XbaI and BamHI to release the P450-1 or P450-2 sequences.

The p35SS vector, described above, and the isolated sweetgum P450-1 or P450-2 fragments were then ligated to make GLS expression cassettes containing the constitutive promoter.

V. INSERTING THE EXPRESSION CASSETTE INTO THE GYMNOSPERM GENOME

There are a number of methods by which the GSL expression cassette may be inserted into a target gymnosperm cell. One method of inserting the expression cassette into the gymnosperm is by micro-projectile bombardment of gymnosperm cells. For example, embryogenic tissue cultures of loblolly pine may be initiated from immature zygotic embryos. Tissue is maintained in an undifferentiated state on semi-solid proliferation medium. For transformation, embryogenic tissue is s; suspended in liquid proliferation medium. Cells are then sieved through, a preferably 40 mesh screen, to separate small, densely cytoplasmic cells from large vacuolar cells.

After separation, a portion of the liquid cell suspension fraction is vacuum deposited onto filter paper and placed on semi-solid proliferation medium. The prepared gymnosperm target cells are then grown for several days on filter paper discs in a petri dish.

A 1:1 mixture of plasmid DNA containing the selectable marker expression cassette and plasmid DNA containing the P450-1 expression cassette may be precipitated with gold to form microprojectiles. The microprojectiles are rinsed in absolute ethanol and aliqots are dried onto a suitable macrocarrier such as the macrocarrier available from BioRad in Hercules, Calif.

Prior to bombardment, embryogenic tissue is preferably desiccated under a sterile laminar-flow hood. The desiccated tissue is transferred to semi-solid proliferation medium. The prepared microprojectiles are accelerated from the macrocarrier into the desiccated target cells using a suitable apparatus such as a BioRad PDS-1000/HE particle gun. In a preferred method, each plate is bombarded once, rotated 180 degrees, and bombarded a second time. Preferred bombardment parameters are 1350 psi rupture disc pressure, 6 mm distance from the rupture disc to macrocarrier (gap distance), 1 cm macrocarrier travel distance, and 10 cm distance from macrocarrier stopping screen to culture plate (microcarrier travel distance). Tissue is then transferred to semi-solid proliferation medium containing a selection agent, such as hygromycin B, for two days after bombardment.

Other methods of inserting the GSL expression cassette include use of silicon carbide whiskers, transformed protoplasts, Agrobacterium vectors and electroporation.

VI. IDENTIFYING TRANSFORMED CELLS

In general, insertion of the GSL expression cassette will typically be carried out in a mass of cells and it will be necessary to determine which cells harbor the recombinant DNA molecule containing the GSL expression cassette. Transformed cells are first identified by their ability to grow vigorously on a medium containing an antibiotic which is toxic to non-transformed cells. Preferred antibiotics are kanamycin and hygromycin B. Cells which grow vigorously on antibiotic containing medium are further tested for presence of either portions of the plasmid vector, the syringyl lignin genes in the GSL expression cassette; e.g. the angiosperm bi-OMT, 4CL, P450-1 or P450-2 gene, or by testing for presence of other fragments in the GSL expression cassette. Specific methods which can be used to test for presence of portions of the GSL expression cassette include Southern blotting with a labeled complementary probe or PCR amplification with specific complementary primers. In yet another approach, an expressed syringyl lignin enzyme can be detected by Western blotting with a specific antibody, or by assaying for a functional property such as the appearance of functional enzymatic activity.

VII. PRODUCTION OF A GYMNOSPERM PLANT FROM THE TRANSFORMED GYMNOSPERM CELL

Once transformed embryogenic cells of the gymnosperm have been identified, isolated and multiplied, they may be grown into plants. It is expected that all plants resulting from transformed cells will contain the GSL expression cassette in all their cells, and that wood in the secondary growth stage of the mature plant will be characterized by the presence of syringyl lignin.

Transgenic embryogenic cells are allowed to replicate and develop into a somatic embryo, which are then converted into a somatic seedling.

VIII. IDENTIFICATION, PRODUCTION AND INSERTION OF A GL mRNA ANTI-SENSE SEQUENCE

In addition to adding ASL DNA sequences, anti-sense sequences may be incorporated into a gymnosperm genome, via GSL expression cassettes, in order to suppress formation of the less preferred native gymnosperm lignin. To this end, the gymnosperm lignin gene is first located and sequenced in order to determine its nucleotide sequence. Methods for locating and sequencing amino acids which have been previously discussed may be employed. For example, if the gymnosperm lignin gene has already been purified, standard sequencing methods may be employed to determine the DNA nucleic acid sequence.

If the gymnosperm lignin gene has not been purified and functionally similar DNA or mRNA sequences from similar species are known, those sequences may be compared to identify highly conserved regions and this information used as a basis for the construction of a probe. A gymnosperm cDNA or genomic library can be probed with the above mentioned sequences to locate the gymnosperm lignin cDNA or genomic DNA. Once the gymnosperm lignin DNA is located, it may be sequenced using standard sequencing methods.

After the DNA sequence has been obtained for a gymnosperm lignin sequence, the complementary anti-sense strand is constructed and incorporated into an expression cassette. For example, the GL mRNA anti-sense sequence may be fused to a promoter region to form an expression cassette as described above. In a preferred method, the GL mRNA anti-sense sequence is incorporated into the previously discussed GSL expression cassette which is inserted into the gymnosperm genome as described above.

IX. INCLUSION OF CYTOCHROME P450 REDUCTASE (CPR) TO ENHANCE BIOSYNTHESIS OF SYRINGYL LIGNIN IN GYMNOSPERMS

In the absence of external cofactors such as NADPH (an electron donor in reductive biosyntheses), certain angiosperm lignin genes such as the P450 genes may remain inactive or not achieve full or desired activity after insertion into the genome of a gymnosperm. Inactivity or insufficient activity can be determined by testing the resulting plant which contains the P450 genes for the presence of syringyl lignin in secondary growth. It is known that cytochrome P450 reductase (CPR) may be involved in promoting certain reductive biochemical reactions, and may activate the desired expression of genes in many plants. Accordingly, if it is desired to enhance the expression of the angiosperm syringyl lignin genes in the gymnosperm, CPR may be inserted in the gymnosperm genome. In order to express CPR, the DNA sequence of the enzyme is ligated to a constitutive promoter or, for a specific species such as loblolly pine, xylem-specific lignin promoters such as PAL, 4CL1B or 4CL3B to form an expression cassette. The expression cassette may then be inserted into the gymnosperm genome by various methods as described above.

X. EXAMPLES

The following non-limiting examples illustrate further aspects of the invention. In these examples, the angiosperm is Liquidambar styraciflua (L.)[sweetgum] and the gymnosperm is Pinus taeda (L.)[loblolly pine]. The nomenclature for the genes referred to in the examples is as follows:

Genes Biochemical Name 4CL (angiosperm) 4-coumarate CoA ligase bi-OMT (angiosperm) bifunctional-O-methyl transferase FA5HP450-1 (angiosperm) Cytochrome P450 P450-2 (angiosperm) Cytochrome P450 PAL (gymnosperm) phenylalanine ammonia-lyase 4CL1B (gymnosperm) 4-coumarate CoA ligase 4CL3B (gymnosperm) 4-coumarate CoA ligase

Example 1 Isolating and Sequencing bi-OMT and 4CL Genes from an Angiosperm

A cDNA library for Sweetgum was constructed in Lambda ZAPII, available from Stratagene, of LaJolla, Calif., using poly(A)+RNA isolated from Sweetgum xylem tissue. Probes for bi-OMT and 4CL were obtained through reverse transcription of their mRNAs and followed by double PCR using gene-specific primers which were designed based on the OMT and CCL cDNA sequences obtained from similar genes cloned from other species.

Three primers were used for amplifying OMT fragments. One was an oligo-dT primer. One was a bi-OMT, (which was used to clone gene fragments through modified differential display technique, as described below in Example 2) and the other two were degenerate primers, which were based on the conserved sequences of all known OMTs. The two degenerate primers were derived based on the following amino acid sequences:

(primer #22) (SEQ ID 12) 5′-Gly Gly Met Ala Thr Tyr Cys Cys Ala Thr Thr Tyr Ala Ala Cys Ala Ala Gly Gly Cys-3′ and (primer #23) (SEQ ID 13) 3′-Ala Ala Ala Gly Ala Gly Ala Gly Asn Ala Cys Asn Asn Ala Asn Asn Ala Asn Gly Ala-5′.

A 900 by PCR product was produced when oligo-dT primer and primer #22 were used, and a 550 by fragment was produced when primer numbers 22 and 23 were used.

Three primers were used for amplifying CCL fragments. They were derived from the following amino acid sequences:

(primer R1S) (SEQ ID 14) 5′-Thr Thr Gly Gly Ala Thr Cys Cys Gly Gly Ile Ala Cys Ile Ala Cys Ile Gly Gly Ile Tyr Thr Ile Cys Cys Ile Ala Ala Arg Gly Gly-3′ (primer H1S) (SEQ ID 15) 5′-Thr Thr Gly Gly Ala Thr Cys Cys Gly Thr Ile Gly Thr Ile Gly Cys Ile Cys Ala Arg Cys Ala Arg Gly Thr Ile Gly Ala Tyr Gly Gly-3′ and (primer R2A) (SEQ ID 16) 3′-Cys Cys Ile Cys Thr Tyr Thr Ala Asp Ala Cys Arg Thr Ala Asp Gly Cys Ile Cys Cys Ala Gly Cys Thr Gly Thr Ala-5′

R1S and H1S were both sense primers. Primer R2A was an anti-sense primer. A 650 by fragment was produced if R1S and R2A primers were used and a 550 by fragment was produced when primers H1S and R2A were used. The sequence of these three primers were derived from conserved sequences for plant CCLs.

The reverse transcription-double PCR cloning technique used for these examples consisted of adding 10 μgf DNA-free total RNA in 25 lDEPC-treated water to a microfuge tube. Next, the following solutions were added:

-   -   a. 5× Reverse transcript buffer 8.0 μl,     -   b. 0.1 MDTT 4.0 μl     -   c. 10 mM dNTP 2.0 μl     -   d. 100 μM oligo-dT primers 8.0 μl     -   e. Rnasin 2.0 μl     -   f. Superscript II 1.0 μl

After mixing, the tube was incubated at a temperature of 42° C. for one (1) hour, followed by incubation at 70° C. for fifteen (15) minutes. Forty (40) μl of 1N NaOH was added and the tube was further incubated at 68° C. for twenty (20) minutes. After the incubation periods, 80 μl of 1N HCl was added to the reaction mixture. At the same time, 17 μl NaOAc, 5 μl glycogen and 768 μl of 100% ethanol were added and the reaction mixture was maintained at −80° C. for 15 minutes in order to precipitate the cDNA. The precipitated cDNA was centrifuged at high speed at 4° C. for 15 minutes. The resulting pellet was washed with 70% ethanol and then dried at room temperature, and then was dissolved in 20 μl of water.

The foregoing procedure produced purified cDNA which was used as a template to carry out first round PCR using primers #22 and oligo-dT for cloning OMT cDNA and primer R1S and R2A for cloning 4CL cDNA. For the first round PCR, a master mix of 50 μl for each reaction was prepared. Each 50 μl mixture contained:

-   -   a. 10× buffer 5 μl     -   b. 25 mM MgCl₂ 5 μl     -   c. 100 μM sense primer 1 μl (primer #22 for OMT and primer R1S         for CCL).     -   d. 100 μl anti-sense primer 1 μl (oligo-dT primer for OMT and         R2A for CCL).     -   e. 10 mM dNTP 1 μl     -   f. Taq. DNA polymerase 0.5 μl

Of this master mix, 48 μl was added into a PCR tube containing 2 μl of cDNA for PCR. The tube was heated to 95° C. for 45 seconds, 52° C. for one minute and 72° C. for two minutes. This temperature cycle was repeated for 40 cycles and the mixture was then held at 72° C. for 10 minutes.

The cDNA fragments obtained from the first round of PCR were used as templates to perform the second round of PCR using primers 22 and 23 for cloning bi-OMT cDNA and primer H1S and R2A for cloning 4CL cDNA. The second round of PCR conditions were the same as the first round.

The desired cDNA fragment was then subcloned and sequenced. After the second round of PCR, the product with the predicted size was excised from the gel and ligated into a pUC19 vector, available from Clonetech, of Palo Alto, Calif., and then transformed into DH5.alpha., an E. coli strain, available from Gibco BRL, of Gaithersburg, Md. After the inserts had been checked for correct size, the colonies were isolated and plasmids were sequenced using a Sequenase kit available from USB, of Cleveland, Ohio. The sequences are shown in FIG. 2 (SEQ ID 5 and 6) and FIG. 3 (SEQ ID 7 and 8).

Example 2 Alternative Isolation Method of Angiosperm bi-OMT Gene

As previously mentioned, one bi-OMT clone was produced via modified differential display technique. This method is another type of reverse transcription-PCR, in which DNA-free total RNA was reverse transcribed using oligo-dT primers with a single base pair anchor to form cDNA. The oligo-dT primers used for reverse transcription of mRNA to synthesize cDNA were:

4 T11A: TTTTTTTTTTTTTTA, (SEQ ID 17) T11C: TTTTTTTTTTTTTTC, (SEQ ID 18) and T11G: TTTTTTTTTTTTTTG, (SEQ ID 19)

These cDNAs were then used as templates for radioactive PCR which was conducted in the presence of the same oligo-dT primers as listed above, a bi-OMT gene-specific primer and 35S-dATP. The OMT gene-specific primer was derived from the following amino acid sequence:

-   -   5′-Cys Cys Asn Gly Gly Asn Gly Gly Ser Ala Arg Gly Ala-3′. (SE         ID 20)

The following PCR reaction solutions were combined in a microfuge tube:

-   -   a. H₂O 9.2 μl,     -   b. Taq Buffer 2.0 μl     -   c. dNTP (25 μM) 1.6 μl     -   d. Primers (5 μM) 2 μl, for each primer     -   e. ³⁵S-dATP 1 μl     -   f. Taq. pol. 0.2 μl     -   g. cDNA 2.0 μl.

The tube was heated to a temperature of 94° C. and held for 45 seconds, then at 37° C. for 2 minutes and then 72° C. for 45 seconds for forty cycles, followed by a final reaction at 72° C. for 5 minutes.

The amplified products were fractionated on a denaturing polyacrylamide sequencing gel and autoradiography was used to identify and excise the fragments with a predicted size. The designed OMT gene-specific primer had a sequence conserved in a region toward the 3′-end of the OMT cDNA sequence. This primer, together with oligo-dT, was amplified into a OMT cDNA fragment of about 300 bp.

Three oligo-dTs with a single base pair of A, C or G, respectively, were used to pair with the OMT gene-specific primer. Eight potential OMT cDNA fragments with predicted sizes of about 300 by were excised from the gels after several independent PCR rounds using different combinations of oligo-dT and OMT gene-specific oligo-nucleotides as primers.

The OMT cDNA fragments were then re-amplified. A Southern blot analysis was performed for the resulting cDNAs using a 360 base-pair, ³²P radio-isotope labeled, aspen OMT cDNA 3′-end fragment as a probe to identify the cDNA fragments having a strong hybridization signal, under low stringency conditions. Eight fragments were identified. Out of these eight cDNA fragments, three were selected based on their high hybridization signal for sub-cloning and sequencing. One clone, LsOMT3′-1, (where the “Ls” prefix indicates that the clone was derived from the Liquidambar styraciflua (L.) genome) was confirmed to encode bi-OMT based on its high homology to other lignin-specific plant OMTs at both nucleotide and amino acid sequence levels.

A cDNA library was constructed in Lambda ZAP II, available from Stratagene, of LaJolla, Calif., using 5 mg poly(A)+RNA isolated from sweetgum xylem tissue. The primary library consisting of approximately 0.7×10⁶ independent recombinants was amplified and approximately 10⁵ plaque-forming-units (pfu) were screened using a homologous 550 base-pair probe. The hybridized filter was washed at high stringency (0.25×SSC, 0.1% SDS, 65° C.) conditions. The colony containing the bi-OMT fragment identified by the probe was eluted and the bi-OMT fragment was produced. The sequence as illustrated in FIG. 2 (SEQ ID 5 and 6) was obtained.

Example 3 Isolating and Producing the DNA which Codes for the Angiosperm P450-1 Gene

In order to find putative P450 cDNA fragments as probes for cDNA library screening, a highly degenerated sense primer based on the amino acid sequence of 5′-Glu, Glu, Phe, Arg, Pro, Glu, Arg-3′ was designed based on the conserved regions found in some plant P450 proteins. This conserved domain was located upstream of another highly conserved region in P450 proteins, which had an amino acid sequence of 5′-Phe Gly Xaa Gly Xaa Xaa Cys Xaa Gly-3′ (SEQ ID 21). This primer was synthesized with the incorporation of an XboI restriction site to give a 26-base-pair oligomer with a nucleotide sequence of 5′ ATG TGC AGT TTT TTT TTT TTT TIT TT-3′ (SEQ ID 22).

This primer and the oligo-dT-XhoI primer were then used to perform PCR reactions with the sweetgum cDNA library as a template. The cDNA library was constructed in Lambda ZAPII, available from Stratagene, of LaJolla, Calif., using poly(a)+RNA isolated from Sweetgum xylem tissue. Amplified fragments of 300 to 600 by were obtained. Because the designed primer was located upstream of the highly conserved P450 domain, this design distinguished whether the PCR products were P450 gene fragments depending on whether they contained the highly conserved amino acid domain.

All the fragments obtained from the PCR reaction were then cloned into a pUC19 vector, available from Stratagene, of LaJolla, Calif., and transformed into a DH5.alpha. E. coli strain, available from Gibco BRL, of Gaithersburg, Md.

Twenty-four positive colonies were obtained and sequenced. Sequence analysis indicated four groupings within the twenty-four colonies. One was C4H, one was an unknown P450 gene, and two did not belong to P450 genes. Homologies of P450 genes in different species are usually more than 80%. Because the homologies between the P450 gene families found here were around 40%, the sequence analysis indicated that a new P450 gene family was sequenced. Moreover, since this P450 cDNA was isolated from xylem tissue, it was highly probable that this P450 gene was P450-1.

The novel sweetgum P450 cDNA fragment was used as a probe to screen a full length cDNA encoding for P450-1. Once the P450-1 gene was located it was sequenced. The length of the P450-1 cDNA is 1707 by and it contains 45 by of 5′ non-coding region and 135 by of 3′ non-coding region. The deduced amino acid sequence also indicates that this P450 cDNA has a hydrophobic core at the N-terminal, which could be regarded as a leader sequence for c-translational targeting to membranes during protein synthesis. At the C-terminal region, there is a heme binding domain that is characteristic of all P450 genes. The P450-1 sequence, as illustrated in FIG. 4 (SEQ ID 1 and 2), was produced, according to the above described methods.

Example 4 Isolating and Producing the DNA which Codes for the Angiosperm P450-2 Gene

By using similar strategy of synthesizing PCR primers from the published literature for hydroxylase genes in plants, another full length P450 cDNA has been isolated that shows significant similarity with a putitive FSH clone from Arabidopsis (Meyers et al. 1996: PNAS 93, 6869-6874). This cloned cDNA, designated P450-2, contains 1883 by and encodes an open reading frame of 511 amino acids. The amino acid similarity shared between Arabidopsis FSH and the P450-2 sweetgum clone is about 75%.

To confirm the function of the P450-2 gene, it was expressed in E. coli, strain, DH5 alpha, via pQE vector preparation, according to directions available with the kit. A CO—Fe2+binding assay was also performed to confirm the expression of P450-2 as a functional P450 gene. (Omura & Sato 1964, J. of Biochemistry 239: 2370-2378, Babriac et. al. 1991 Archives of Biochemistry and Biophysics 288:302-309). The CO—Fe2+binding assay showed a peak at 450 nm which indicates that P450-2 has been overexpressed as a functional P450 gene.

The P450-2 protein was further purified for production of antibodies in rabbits, and antibodies have been successfully produced. In addition, Western blots show that this antibody is specific to the membrane fraction of sweetgum and aspen xylem extract. When the P450-2 antibody was added to a reaction mixture containing aspen xylem tissue, enzyme inhibition studies showed that the activity of P450 in aspen was reduced more than 60%, a further indication that P450-2 performs a p450 like function. Recombinant P450-2 protein co-expressed with Arabidopsis CPR protein in a baculovirus expression system hydroxylated ferulic acid (specific activity: 7.3 pKat/mg protein), cinnaminic acid (specific activity: 25 pKat/mg protein, and p-coumeric acid (specific activity 3.8 pKat/ng protein). The P450-2 enzyme which may be referred to as C4C3F5-H appears to be a broad spectrum hydroxylase in the phenyproponoid pathway in plants FIG. 5 (SEQ ID 3 and 4) illustrates the P450-2 sequence.

Example 5 Identifying Gymnosperm Promoter Regions

In order to identify gymnosperm promoter regions, sequences from loblolly pine PAL and CL1B and 4CL3B lignin genes were used as primers to screen the loblolly pine genomic library, using the GenomeWalker Kit. The loblolly pine PAL primer sequence was obtained from the GenBank, reference number U39792. The loblolly pine 4CL1B primer sequences were also obtained from the gene bank, reference numbers U39404 and U39405.

The loblolly pine genomic library was constructed in Lambda DashII, available from Stratagene, of LaJolla, Calif. 3×10⁶ phage plaques from the genomic library of loblolly pine were screened using both the above mentioned PAL cDNA and 4CL (PCR clone) fragments as probes. Five 4CL clones were obtained after screening. Lambda DNAs of two 4CL of the five 4CL clones obtained after screening were isolated and digested by EcoRV, Pstd, SalI and XbaI for Southern analysis. Southern analysis using 4CL fragments as probes indicated that both clones for the 4CL gene were identical. Results from further mapping showed that none of the original five 4CL clones contained promoter regions. When tested, the PAL clones obtained from the screening also did not contain promoter regions.

In a second attempt to clone the promoter regions associated with the PAL and 4CL a Universal GenomeWalker.™ kit, available from CLONETECH, was used. In the process, total DNA from loblolly pine was digested by several restriction enzymes and ligated into the adaptors (libraries) provided with the kit. Two gene-specific primers for each gene were designed (GSP1 and 2). After two rounds of PCR using these primers and adapter primers of the kit, several fragments were amplified from each library. A 1.6 kb fragment and a 0.6 kb fragment for PAL gene and a 2.3 kb fragment (4CL1B) and a 0.7 kb fragment (4CL3B) for the 4CL gene were cloned, sequenced and found to contain promoter regions for all three genes. See FIG. 6 (SEQ ID 10), 7 (SEQ ID 11) and 8 (SEQ ID 9).

Example 6 Fusing the ASL DNA Sequence to a Constitutive Promoter Region and Inserting the Expression Cassette into a Gymnosperm Genome

As a first step, a ASL DNA sequence, P450-1, was fused with a constitutive promoter region according to the methods described in the above Section IV to form an P450-1 expression cassette. A second ASL DNA sequence, P450-2, was then fused with a constitutive promoter in the same manner to form an P450-2 expression cassette. The P450-1 expression cassette was inserted into the gymnosperm genome by micro-projectile bombardment. Embryogenic tissue cultures of loblolly pine were initiated from immature zygotic embryos. The tissue was maintained in an undifferentiated state on semi-solid proliferation medium, according to methods described by Newton et al. TAES Technical Publication “Somatic Embryogenesis in Slash Pine”, 1995 and Keinonen-Mettala et al. 1996, Scand. J. For. Res. 11: 242-250.

After separation, 5 ml of the liquid cell suspension fraction which passes through the 40 mesh screen was vacuum deposited onto filter paper and placed on semi-solid proliferation medium. The prepared gymnosperm target cells were then grown for 2 days on filter paper discs placed on semi-solid proliferation medium in a petri dish. These target cell were then bombarded with plasmid DNA containing the P450-1 expression cassette and an expression cassette containing a selectable marker gene encoding the enzyme which confers resistance to the antibiotic hygromycin B. A 1:1 mixture of selectable marker expression cassette and plasmid DNA containing the P450-1 expression cassette is precipitated with gold (1.5-3.0 microns) as described by Sanford et al. (1992). The DNA-coated microprojectiles were rinsed in absolute ethanol and aliquots of 10 μl (5 μg DNA/3 mg gold) were dried onto a macrocarrier, such as those available from BioRad (Hercules, Calif.).

Prior to bombardment, embryogenic tissue was desiccated under a sterile laminar-flow hood for 5 minutes. The desiccated tissue was transferred to semi-solid proliferation medium. The microprojectiles were accelerated into desiccated target cells using a BioRad PDS-1000/HE particle gun.

Each plate was bombarded once, rotated 180 degrees, and bombarded a second time. Preferred bombardment parameters were 1350 psi rupture disc pressure, 6 mm distance from the rupture disc to macrocarrier (gap distance), 1 cm macrocarrier travel distance, and 10 cm distance from macrocarrier stopping screen to culture plate (microcarrier travel distance). Tissue was then transferred to semi-solid proliferation medium containing hygromycin B for two days after bombardment.

The P450-2 expression cassette was inserted into the gymnosperm genome according to the same procedures.

Example 7 Selecting Transformed Target Cells

After insertion of the P450-1 expression cassette and the selectable marker expression cassette into the gymnosperm target cells as described in Example 6, transformed cells were selected by exposure to an antibiotic that causes mortality of any cells not containing the GSL expression cassette. Forty independent cell lines were established from cultures cobombarded with an expression cassette containing a hygromycin resistance gene construct and the P450-1 construct. These cell lines include lines Y2, Y17, Y7 and 04, as discussed in more detail below.

PCR techniques were then used to verify that the P450-1 gene had been successfully integrated into the genomes of the established cell lines by extracting genomic DNA using the Plant DNAeasy kit, available from Quaigen. 200 ng DNA from each cell line were used for each PCR reaction. Two P450-1 specific primers were designed to perform a PCR reaction with a 600 by PCR product size. The primers were:

LsP450-im1-S primer: ATGGCTTTCCTTCTAATACCCATCTC, (SEQ ID 23) and LsP450-im1-A primer: GGGTGTAATGGACGAGCAAGGACTTG. (SEQ ID 24)

Each PCR reaction (100 μl) consisted of 75 μl H2O, 1 μl MgCl (25 mM), 10 μl PCR buffer 1 μl 10 mM dNTPs, and 10 μl DNA. 100 μl oil was layered on the top of each reaction mix. Hot start PCR was done as follows: PCR reaction was incubated at 95 degrees C. for 7 minutes and 1 μl each of both LsP450-im1-S and LsP450-im1-A primers (100 μM stock) and 1 μl of Taq polymerase were added through oil in each reaction. The PCR program used was 95 degrees C. for 1.5 minutes, 55 degrees C. for 45 sec and 72 degrees C. for 2 minutes, repeated for 40 cycles, followed by extension at 72 degrees C. for 10 minutes.

The above PCR products were employed to determine if gymnosperm cells contained the angiosperm lignin gene sequences. With reference to FIG. 9, PCR amplification was performed using template DNA from cells which grew vigorously on hygromycin B-containing medium. The PCR products were electrophoresed in an agarose gel containing 9 lanes. Lanes 14 contained PCR amplification of products of the Sweetgum P450-1 gene from a non-transformed control and transgenic loblolly pine cell lines. Lane 1 contained the non-transformed control PT52. Lane 2 contained transgenic line Y2. Lane 3 contained transgenic line Y17 and Lane 4 contained the plasmid which contains the expression cassette pSSLsP4501-im-s. Lanes 2 through 4 all contain an amplified fragment of about 600 bp, indicating that the P450-1 gene has been successfully inserted into transgenic cell lines Y2 and Y17.

Lane 5 contained a DNA size marker Phi 174/HaeII (BRL). The top four bands in this lane indicate molecular sizes of 1353, 1078, 872 and 603 bp.

Lanes 6-9 contained PCR amplification products of hygromycin B gene from non-transformed control and transgenic loblolly pine cell lines. Lane 6 contained the non-transformed control lane referenced to as PTS. Lane 7 contained transgenic line Y7. Lane 8 contained transgenic line 04. Lane 9 contained the plasmid which includes the expression cassette containing the gene encoding the enzyme which confers resistance to the antibiotic hygromycin B. Lanes 7-9 all show an amplified fragment of about 1000 bp, indicating that the hygromycin gene has been successfully inserted into transgenic lines Y7 and 04.

These PCR results confirmed the presence of P450-1 and hygromycin resistance gene in transformed loblolly pine cell cultures. The results obtained from the PCR verification of 4 cell lines, and similar tests with the remaining 36 cell lines, confirm stable integration of the P450-1 gene and the hygromycin B gene in 25% of the 40 cell lines.

In addition, loblolly pine embryogenic cells which have been co-bombarded with the P450-2 and hygromycin B expression cassettes, are growing vigorously on hygromycin selection medium, indicating that the P450-2 expression cassette was successfully integrated into the gymnosperm genome.

Although various embodiments and features of the invention have been described in the foregoing detailed description, those of ordinary skill will recognize the invention is capable of numerous modifications, rearrangements and substitutions without departing from the scope of the invention as set forth in the appended claims. For example, in the case where the lignin DNA sequence is transcribed and translated to produce a functional syringyl lignin gene, those of ordinary skill will recognize that because of codon degeneracy a number of polynucleotide sequences will encode the same gene. These variants are intended to be covered by the DNA sequences disclosed and claimed herein. In addition, the sequences claimed herein include those sequences with encode a gene having substantial functional identity with those claimed. Thus, in the case of syringyl lignin genes, for example, the DNA sequences include variant polynucleotide sequences encoding polypeptides which have substantial identity with the amino acid sequence of syringyl lignin and which show syringyl lignin activity in gymnosperms. 

1-45. (canceled)
 46. A method for modifying the genome of a plant comprising (a) fusing one or more DNA sequences to a promoter sequence selected from the group consisting of SEQ ID NO: 10 and SEQ ID NO: 11 to form an expression cassette; and (b) inserting the expression cassette into the plant to thereby produce a modified genome in the plant, wherein the one or more DNA sequences are expressed in the plant.
 47. The method of claim 46, wherein the one or more DNA sequences are angiosperm DNA sequences.
 48. The method of claim 46, wherein the one or more DNA sequences are a genetic sequence which codes for an anti-sense mRNA.
 49. The method of claim 48, wherein the anti-sense mRNA is a gymnosperm genetic sequence which codes for the 4-coumarate CoA ligase (4CL) gene.
 50. The method of claim 46, wherein the one or more DNA sequences encode one or more proteins selected from the class consisting of 4-coumarate CoA ligase (4CL), bifunctional-O-methyl transferase (bi-OMT) and ferulic acid-5-hydroxylase (FA5H).
 51. The method of claim 46, wherein the plant is a gymnosperm.
 52. The method of claim 51, wherein the gymnosperm is Pinus taeda L.
 53. The method of claim 46, wherein the expression cassette is inserted into the plant genome by way of the transformation vector Agrobacterium.
 54. The method of claim 53, wherein the Agrobacterium is Agrobacterium tumefaciens EH101.
 55. The method of claim 46, wherein the expression cassette is inserted into the plant genome via direct DNA delivery to a target cell.
 56. The method of claim 46, wherein expression cassette is inserted into the plant genome by micro-projectile bombardment of a plant cell.
 57. The method of claim 46, wherein the expression cassette is inserted into the plant genome by electroporation of a plant cell.
 58. The method of claim 46, wherein the expression cassette is inserted into the plant genome via silicon carbide whiskers.
 59. The method of claim 46, wherein the expression cassette is inserted into the plant genome via transformed protoplast.
 60. The method of claim 46 further comprising inserting a selectable marker into the expression cassette.
 61. The method of claim 60, wherein the selectable marker is selected from the group consisting of kanamycin and hygromycin B. 